A novel measure to analyze protein structures: Aspect ratio in protein alpha shapes

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dc.authorscopusid8754351000
dc.authorscopusid57224176922
dc.authorscopusid23481439700
dc.authorscopusid57224169998
dc.contributor.authorBağcı, Elife Zerrin
dc.contributor.authorSenguler-Ciftci, F.
dc.contributor.authorÇiftçi, Ünver
dc.contributor.authorDemir, A.
dc.date.accessioned2022-05-11T14:02:47Z
dc.date.available2022-05-11T14:02:47Z
dc.date.issued2021
dc.departmentFakülteler, Fen Edebiyat Fakültesi, Biyoloji Bölümü
dc.departmentFakülteler, Fen Edebiyat Fakültesi, Matematik Bölümü
dc.description.abstractProteins' three-dimensional (3D) structures are analyzed traditionally using geometric descriptors such as torsional angles and inter-atomic distances. In this study a measure that is borrowed from computational geometry, aspect ratio of each tetrahedron in alpha shapes of proteins, is utilized. This geometric descriptor differentiates alpha and beta structural classes of proteins when combined with principal components analysis. The method converts the structures of individual proteins, 3D coordinates of the atoms, to points on a plane. It has a high degree of accuracy in differentiating R and T structures of hemoglobin. Therefore, it is anticipated that the geometric measure can be used successfully in a method that is extended to solve classification problems in machine learning. © 2021 Wiley Periodicals LLC.
dc.identifier.doi10.1002/prot.26148
dc.identifier.endpage1276
dc.identifier.issn0887-3585
dc.identifier.issue10en_US
dc.identifier.pmid33993533
dc.identifier.scopus2-s2.0-85107157855
dc.identifier.scopusqualityQ1
dc.identifier.startpage1270
dc.identifier.urihttps://doi.org/10.1002/prot.26148
dc.identifier.urihttps://hdl.handle.net/20.500.11776/4487
dc.identifier.volume89
dc.identifier.wosWOS:000658040700001
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorBağcı, Elife Zerrin
dc.institutionauthorÇiftçi, Ünver
dc.language.isoen
dc.publisherJohn Wiley and Sons Inc
dc.relation.ispartofProteins: Structure, Function and Bioinformatics
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.subjectalpha shape
dc.subjectaspect ratio of tetrahedron
dc.subjectDelaunay triangulation
dc.subjectgeometric descriptors
dc.subjectsphericity
dc.subjectprotein
dc.subjectchemistry
dc.subjectmolecular model
dc.subjectprotein conformation
dc.subjectModels, Molecular
dc.subjectProtein Conformation
dc.subjectProteins
dc.titleA novel measure to analyze protein structures: Aspect ratio in protein alpha shapes
dc.typeArticle

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